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MicroSoft
Just to add to the knowledge base, any time I can't start a game due to not having the correct map or map version I lose mouse control. It's very common for me in Tremulous. I thought it was a known issue as it happens on at least four of my machines that have Tremulous installed including both Windows and Linux.
Time for MicroSoft Windows.
Linux: ~/.tremulous/base/Mac: ~/Library/Application\ Support/Tremulous/base/Windows: C:\Documents and Settings\username\Local Settings\Application Data\Tremulous\base\